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refactor: vcf2cytosure container #1159

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merged 6 commits into from May 22, 2023
Merged

refactor: vcf2cytosure container #1159

merged 6 commits into from May 22, 2023

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khurrammaqbool
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This PR:

Changed: The base of the container.
Fixed: dependency versions for the installation of vcf2cytosure.

Review and tests:

  • Tests pass
  • Code review
  • New code is executed and covered by tests, and test approve

@khurrammaqbool khurrammaqbool self-assigned this May 17, 2023
@khurrammaqbool khurrammaqbool requested a review from a team May 17, 2023 16:10
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codecov bot commented May 17, 2023 •
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Codecov Report

Patch and project coverage have no change.

Comparison is base (3f1cbce) 99.31% compared to head (41494be) 99.31%.

Additional details and impacted files 
@@           Coverage Diff            @@
##           develop    #1159   +/-   ##
========================================
  Coverage    99.31%   99.31%           
========================================
  Files           29       29           
  Lines         1758     1758           
========================================
  Hits          1746     1746           
  Misses          12       12
Flag Coverage Δ
unittests 99.31% <ø> (ø)

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@khurrammaqbool khurrammaqbool linked an issue May 17, 2023 that may be closed by this pull request
vcf2cytosure container failed #1158
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ivadym
ivadym reviewed May 22, 2023
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I ran the container build again on your PR and it seems to have resolved itself:

https://github.com/Clinical-Genomics/BALSAMIC/actions/runs/5001681295/jobs/9044597000?pr=1126

@khurrammaqbool
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I ran the container build again on your PR and it seems to have resolved itself:

https://github.com/Clinical-Genomics/BALSAMIC/actions/runs/5001681295/jobs/9044597000?pr=1126

This pull request fixes the versions of the dependencies as we have started to do to build all the containers. It is similar to what is done in #1096. Additionally, I have removed conda, which will make this container more stable, reduce the size and little bit faster to build.

@khurrammaqbool khurrammaqbool changed the title fix: vcf2cytosure container refactor: vcf2cytosure container May 22, 2023
ivadym
ivadym approved these changes May 22, 2023
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Well done ⭐ Nothing major to add, just some small suggestions 👍

BALSAMIC/containers/vcf2cytosure/vcf2cytosure.yaml Outdated Show resolved Hide resolved
BALSAMIC/containers/vcf2cytosure/Dockerfile Outdated Show resolved Hide resolved
BALSAMIC/containers/vcf2cytosure/Dockerfile Outdated Show resolved Hide resolved
BALSAMIC/containers/vcf2cytosure/Dockerfile Outdated Show resolved Hide resolved
BALSAMIC/containers/vcf2cytosure/Dockerfile Outdated Show resolved Hide resolved
@khurrammaqbool
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Thanks you 🙏 @ivadym for the suggestions.

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sonarcloud bot commented May 22, 2023

Kudos, SonarCloud Quality Gate passed!    Quality Gate passed

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities
Security Hotspot A 0 Security Hotspots
Code Smell A 0 Code Smells

No Coverage information No Coverage information
0.0% 0.0% Duplication

@khurrammaqbool khurrammaqbool merged commit f7012ae into develop May 22, 2023
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@khurrammaqbool khurrammaqbool deleted the fix/vcf2cytosure_container branch May 22, 2023 12:30
@khurrammaqbool khurrammaqbool mentioned this pull request Sep 13, 2023
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@ivadym ivadym mentioned this pull request Nov 6, 2023
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@ivadym ivadym ivadym approved these changes

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vcf2cytosure container failed
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